Fig. 4: Bulk RNA sequencing analysis revealed potential molecular mechanisms underlying T-cell motility patterns.
From: Deciphering antigen-specific T cell navigation tactics and cancer immune evasion in co-cultures
A Volcano plot of differentially expressed genes between CTLs co-cultured with OVA cancer cells and those co-cultured with WT cancer cells at 12 h after the co-culture (T12A vs T12). Genes that were significantly up and down regulated in T12A samples, i.e., log2(fold change) > 1 and FDR < 0.05, were shown in red and blue, respectively. B Temporal dynamics of selected up-regulated genes in (A). CTLs at 0, 6, 12 h of the co-culture with OVA or WT cancer cells were filtered and sequenced in two replicates. The Z-score of the corresponding expression of the selected genes were calculated and demonstrated. C Results of the KEGG pathway enrichment analysis of differentially expressed genes shown in (A), where the size of the circle corresponds to the number genes in the specific pathway and the color corresponds to FDR values of the enrichment analysis. D Results of the gene ontology (GO) enrichment analysis of differentially expressed genes shown in (A), where different colors correspond to GO terms for biological process (BP), molecular function (MF) or cellular component (CC). E Volcano plot of differentially expressed genes between OVA and WT cancer cells at 12 h after the co-culture with CTLs (C12A vs C12). Genes that were significantly up and down regulated in C12A samples were shown in red and blue, respectively. F Temporal dynamics of selected up-regulated genes in (E). OVA and WT cancer cells at 0, 6, and 12 h of the co-culture with CTLs were filtered and sequenced in two replicates. The Z-score of the corresponding expression of the selected genes were calculated and demonstrated. G Results of the KEGG pathway enrichment analysis of differentially expressed genes shown in (E). H Results of the gene ontology (GO) enrichment analysis of differentially expressed genes shown in (E).
